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DDX58 DExD/H-box helicase 58 [ Homo sapiens (human) ]

Gene ID: 23586, updated on 23-Apr-2019

Summary

Official Symbol
DDX58provided by HGNC
Official Full Name
DExD/H-box helicase 58provided by HGNC
Primary source
HGNC:HGNC:19102
See related
Ensembl:ENSG00000107201 MIM:609631
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
RIG1; RIGI; RIG-I; RLR-1; SGMRT2
Summary
DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), are putative RNA helicases which are implicated in a number of cellular processes involving RNA binding and alteration of RNA secondary structure. This gene encodes a protein containing RNA helicase-DEAD box protein motifs and a caspase recruitment domain (CARD). It is involved in viral double-stranded (ds) RNA recognition and the regulation of immune response. [provided by RefSeq, Jul 2008]
Annotation information
Note: RARRES3 (Gene ID: 5920) and DDX58 (Gene ID: 23586) share the RIG1/RIG-1 alias in common. RIG1 is a widely used alternative name for DExD/H-box helicase 58 (DDX58), which can be confused with the retinoic acid receptor responder 3 (RARRES3) gene, since they share the same alias. [22 Jan 2019]
Expression
Ubiquitous expression in appendix (RPKM 7.8), spleen (RPKM 7.4) and 25 other tissues See more
Orthologs

Genomic context

See DDX58 in Genome Data Viewer
Location:
9p21.1
Exon count:
18
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 9 NC_000009.12 (32455302..32526324, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (32455300..32526322, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107987059 Neighboring gene solute carrier family 25 member 5 pseudogene 8 Neighboring gene aconitase 1 Neighboring gene uncharacterized LOC105376014 Neighboring gene TOP1 binding arginine/serine rich protein Neighboring gene small integral membrane protein 27 Neighboring gene NADH:ubiquinone oxidoreductase subunit B6 Neighboring gene DNA fragmentation factor subunit beta pseudogene 1

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Vpr vpr HIV-1 Vpr upregulates the gene expression of DDX58 in human monocyte-derived dendritic cells PubMed
vpr HIV-1 Vpr upregulates the gene expression of DDX58 in human monocyte-derived macrophages PubMed
retropepsin gag-pol HIV-1 PR targets and relocalizes RIG-I to an insoluble membrane fraction followed by lysosome-mediated degradation PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Antiviral mechanism by IFN-stimulated genes, organism-specific biosystem (from REACTOME)
    Antiviral mechanism by IFN-stimulated genes, organism-specific biosystemThe ISG proteins generated by IFN pathways plays key roles in the induction of innate and adaptive immune responses.
  • Cytokine Signaling in Immune system, organism-specific biosystem (from REACTOME)
    Cytokine Signaling in Immune system, organism-specific biosystemCytokines are small proteins that regulate and mediate immunity, inflammation, and hematopoiesis. They are secreted in response to immune stimuli, and usually act briefly, locally, at very low concen...
  • Cytosolic DNA-sensing pathway, organism-specific biosystem (from KEGG)
    Cytosolic DNA-sensing pathway, organism-specific biosystemSpecific families of pattern recognition receptors are responsible for detecting foreign DNA from invading microbes or host cells and generating innate immune responses. DAI is the first identified s...
  • Cytosolic DNA-sensing pathway, conserved biosystem (from KEGG)
    Cytosolic DNA-sensing pathway, conserved biosystemSpecific families of pattern recognition receptors are responsible for detecting foreign DNA from invading microbes or host cells and generating innate immune responses. DAI is the first identified s...
  • Deubiquitination, organism-specific biosystem (from REACTOME)
    Deubiquitination, organism-specific biosystemUbiquitination, the modification of proteins by the covalent attachment of ubiquitin (Ub), is a key regulatory mechanism for many many cellular processes, including protein degradation by the 26S pro...
  • Epstein-Barr virus infection, organism-specific biosystem (from KEGG)
    Epstein-Barr virus infection, organism-specific biosystemEpstein-Barr virus (EBV) is a ubiquitous human herpesvirus that is associated with oncogenesis. EBV infection to primary human B lymphocytes leads to induction of EBV-specific HLA-restricted cytotoxi...
  • Epstein-Barr virus infection, conserved biosystem (from KEGG)
    Epstein-Barr virus infection, conserved biosystemEpstein-Barr virus (EBV) is a ubiquitous human herpesvirus that is associated with oncogenesis. EBV infection to primary human B lymphocytes leads to induction of EBV-specific HLA-restricted cytotoxi...
  • Hepatitis B, organism-specific biosystem (from KEGG)
    Hepatitis B, organism-specific biosystemHepatitis B virus (HBV) is an enveloped virus and contains a partially double-stranded relaxed circular DNA (RC-DNA) genome. After entry into hepatocytes, HBV RC-DNA is transported to the nucleus and...
  • Hepatitis C, organism-specific biosystem (from KEGG)
    Hepatitis C, organism-specific biosystemHepatitis C virus (HCV) is a major cause of chronic liver disease. The HCV employ several strategies to perturb host cell immunity. After invasion, HCV RNA genome functions directly as an mRNA in the...
  • Hepatitis C, conserved biosystem (from KEGG)
    Hepatitis C, conserved biosystemHepatitis C virus (HCV) is a major cause of chronic liver disease. The HCV employ several strategies to perturb host cell immunity. After invasion, HCV RNA genome functions directly as an mRNA in the...
  • Herpes simplex infection, organism-specific biosystem (from KEGG)
    Herpes simplex infection, organism-specific biosystemHerpes simplex virus (HSV) infections are very common worldwide, with the prevalence of HSV-1 reaching up to 80%-90%. Primary infection with HSV takes place in the mucosa, followed by the establishme...
  • Herpes simplex infection, conserved biosystem (from KEGG)
    Herpes simplex infection, conserved biosystemHerpes simplex virus (HSV) infections are very common worldwide, with the prevalence of HSV-1 reaching up to 80%-90%. Primary infection with HSV takes place in the mucosa, followed by the establishme...
  • ISG15 antiviral mechanism, organism-specific biosystem (from REACTOME)
    ISG15 antiviral mechanism, organism-specific biosystemInterferon-stimulated gene 15 (ISG15) is a member of the ubiquitin-like (Ubl) family. It is strongly induced upon exposure to type I Interferons (IFNs), viruses, bacterial LPS, and other stresses. On...
  • Immune System, organism-specific biosystem (from REACTOME)
    Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
  • Influenza A, organism-specific biosystem (from KEGG)
    Influenza A, organism-specific biosystemInfluenza is a contagious respiratory disease caused by influenza virus infection. Influenza A virus is responsible for both annual seasonal epidemics and periodic worldwide pandemics. Novel strains ...
  • Influenza A, conserved biosystem (from KEGG)
    Influenza A, conserved biosystemInfluenza is a contagious respiratory disease caused by influenza virus infection. Influenza A virus is responsible for both annual seasonal epidemics and periodic worldwide pandemics. Novel strains ...
  • Innate Immune System, organism-specific biosystem (from REACTOME)
    Innate Immune System, organism-specific biosystemInnate immunity encompases the nonspecific part of immunity tha are part of an individual's natural biologic makeup
  • Interferon Signaling, organism-specific biosystem (from REACTOME)
    Interferon Signaling, organism-specific biosystemInterferons (IFNs) are cytokines that play a central role in initiating immune responses, especially antiviral and antitumor effects. There are three types of IFNs:Type I (IFN-alpha, -beta and others...
  • Measles, organism-specific biosystem (from KEGG)
    Measles, organism-specific biosystemMeasles virus (MV) is highly contagious virus that leads infant death worldwide. Humans are the unique natural reservoir for this virus. It causes severe immunosuppression favouring secondary bacteri...
  • Measles, conserved biosystem (from KEGG)
    Measles, conserved biosystemMeasles virus (MV) is highly contagious virus that leads infant death worldwide. Humans are the unique natural reservoir for this virus. It causes severe immunosuppression favouring secondary bacteri...
  • Metabolism of proteins, organism-specific biosystem (from REACTOME)
    Metabolism of proteins, organism-specific biosystemProtein metabolism comprises the pathways of translation, post-translational modification and protein folding.
  • NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10, organism-specific biosystem (from REACTOME)
    NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10, organism-specific biosystemFas-AssociatedDeathDomain (FADD) and receptor interacting protein 1 (RIP1) are death domain containing molecules that interact with the C-terminal portion of IPS-1 and induce NF-kB through interactio...
  • NF-kappa B signaling pathway, organism-specific biosystem (from KEGG)
    NF-kappa B signaling pathway, organism-specific biosystemNuclear factor-kappa B (NF-kappa B) is the generic name of a family of transcription factors that function as dimers and regulate genes involved in immunity, inflammation and cell survival. There are...
  • NF-kappa B signaling pathway, conserved biosystem (from KEGG)
    NF-kappa B signaling pathway, conserved biosystemNuclear factor-kappa B (NF-kappa B) is the generic name of a family of transcription factors that function as dimers and regulate genes involved in immunity, inflammation and cell survival. There are...
  • Negative regulators of RIG-I/MDA5 signaling, organism-specific biosystem (from REACTOME)
    Negative regulators of RIG-I/MDA5 signaling, organism-specific biosystemAs with other cytokine systems, production of type I IFN is a transient process, and can be hazardous to the host if unregulated, resulting in chronic cellular toxicity or inflammatory and autoimmune...
  • Ovarian tumor domain proteases, organism-specific biosystem (from REACTOME)
    Ovarian tumor domain proteases, organism-specific biosystemHumans have 16 Overian tumour domain (OTU) family DUBs that can be evolutionally divided into three classes, the OTUs, the Otubains (OTUBs), and the A20-like OTUs (Komander et al. 2009). OTU family ...
  • Post-translational protein modification, organism-specific biosystem (from REACTOME)
    Post-translational protein modification, organism-specific biosystemAfter translation, many newly formed proteins undergo further covalent modifications that alter their functional properties and that are essentially irreversible under physiological conditions in the...
  • RIG-I-like Receptor Signaling, organism-specific biosystem (from WikiPathways)
    RIG-I-like Receptor Signaling, organism-specific biosystemViral pathogen RNA are recognized by host helicases called RIG-I-like receptors (RLRs) that include DDX58 (RIG-I), DHX58 (LGP2), IFIH1 (MDA5), SNW1, and DDX17. These RLR proteins then go on to initia...
  • RIG-I-like receptor signaling pathway, organism-specific biosystem (from KEGG)
    RIG-I-like receptor signaling pathway, organism-specific biosystemSpecific families of pattern recognition receptors are responsible for detecting viral pathogens and generating innate immune responses. Non-self RNA appearing in a cell as a result of intracellular ...
  • RIG-I-like receptor signaling pathway, conserved biosystem (from KEGG)
    RIG-I-like receptor signaling pathway, conserved biosystemSpecific families of pattern recognition receptors are responsible for detecting viral pathogens and generating innate immune responses. Non-self RNA appearing in a cell as a result of intracellular ...
  • RIG-I/MDA5 mediated induction of IFN-alpha/beta pathways, organism-specific biosystem (from REACTOME)
    RIG-I/MDA5 mediated induction of IFN-alpha/beta pathways, organism-specific biosystemRIG-I-like helicases (RLHs) the retinoic acid inducible gene-I (RIG-I) and melanoma differentiation associated gene 5 (MDA5) are RNA helicases that recognize viral RNA present within the cytoplasm. F...
  • TRAF3-dependent IRF activation pathway, organism-specific biosystem (from REACTOME)
    TRAF3-dependent IRF activation pathway, organism-specific biosystemIPS-1/MAVS/Cardif/VISA with its TRAF-interaction motif (TIM) directly interacts with TRAF3 and recruits TRAF3 to the RIG-I/MDA5 signaling complex. TRAF3 acts as a scaffold for the assembly of a signa...
  • TRAF6 mediated IRF7 activation, organism-specific biosystem (from REACTOME)
    TRAF6 mediated IRF7 activation, organism-specific biosystemTRAF6 is crucial for both RIG-I- and MDA5-mediated antiviral responses. The absence of TRAF6 resulted in enhanced viral replication and a significant reduction in the production of type I IFNs and IL...
  • TRAF6 mediated NF-kB activation, organism-specific biosystem (from REACTOME)
    TRAF6 mediated NF-kB activation, organism-specific biosystemThe TRAF6/TAK1 signal activates a canonical IKK complex, resulting in the activation of NF-kB as well as MAPK cascades leading to the activation of AP-1. Although TRAF6/TAK1 has been implicated in To...
  • Ub-specific processing proteases, organism-specific biosystem (from REACTOME)
    Ub-specific processing proteases, organism-specific biosystemUb-specific processing proteases (USPs) are the largest of the DUB families with more than 50 members in humans. The USP catalytic domain varies considerably in size and consists of six conserved mo...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Potential readthrough

Included gene: TOPORS

Homology

Clone Names

  • FLJ13599, DKFZp434J1111, DKFZp686N19181

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATP binding IEA
Inferred from Electronic Annotation
more info
 
double-stranded DNA binding IEA
Inferred from Electronic Annotation
more info
 
double-stranded RNA binding IDA
Inferred from Direct Assay
more info
PubMed 
double-stranded RNA binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
double-stranded RNA binding TAS
Traceable Author Statement
more info
PubMed 
helicase activity IEA
Inferred from Electronic Annotation
more info
 
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
single-stranded RNA binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
ubiquitin protein ligase binding IPI
Inferred from Physical Interaction
more info
PubMed 
zinc ion binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
RIG-I signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
cellular response to exogenous dsRNA IMP
Inferred from Mutant Phenotype
more info
PubMed 
cytoplasmic pattern recognition receptor signaling pathway in response to virus TAS
Traceable Author Statement
more info
PubMed 
defense response to virus IDA
Inferred from Direct Assay
more info
PubMed 
defense response to virus TAS
Traceable Author Statement
more info
 
detection of virus IDA
Inferred from Direct Assay
more info
PubMed 
innate immune response IMP
Inferred from Mutant Phenotype
more info
PubMed 
innate immune response TAS
Traceable Author Statement
more info
 
negative regulation of type I interferon production TAS
Traceable Author Statement
more info
 
positive regulation of DNA-binding transcription factor activity IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of defense response to virus by host IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of gene expression IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of granulocyte macrophage colony-stimulating factor production IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of interferon-alpha production IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of interferon-alpha production IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of interferon-alpha secretion IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of interferon-beta production IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of interferon-beta production IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of interferon-beta secretion IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of interleukin-6 production IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of interleukin-6 secretion IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of interleukin-8 production IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of myeloid dendritic cell cytokine production ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of response to cytokine stimulus IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of tumor necrosis factor secretion IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein deubiquitination TAS
Traceable Author Statement
more info
 
regulation of cell migration IDA
Inferred from Direct Assay
more info
PubMed 
regulation of type III interferon production TAS
Traceable Author Statement
more info
PubMed 
response to exogenous dsRNA ISS
Inferred from Sequence or Structural Similarity
more info
 
response to virus TAS
Traceable Author Statement
more info
PubMed 
viral process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
actin cytoskeleton IDA
Inferred from Direct Assay
more info
PubMed 
bicellular tight junction IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
 
cytosol TAS
Traceable Author Statement
more info
 
ruffle membrane IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
probable ATP-dependent RNA helicase DDX58
Names
DEAD (Asp-Glu-Ala-Asp) box polypeptide 58
DEAD box protein 58
DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide
RNA helicase RIG-I
retinoic acid-inducible gene 1 protein
retinoic acid-inducible gene I protein
NP_055129.2

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_046918.1 RefSeqGene

    Range
    5001..76023
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_014314.4NP_055129.2  probable ATP-dependent RNA helicase DDX58

    See identical proteins and their annotated locations for NP_055129.2

    Status: REVIEWED

    Source sequence(s)
    AA862613, AF038963, AL161783, BC070029, DN998145
    Consensus CDS
    CCDS6526.1
    UniProtKB/Swiss-Prot
    O95786
    Related
    ENSP00000369213.2, ENST00000379883.3
    Conserved Domains (4) summary
    cd08817
    Location:100189
    CARD_RIG-I_r2; Caspase activation and recruitment domain found in RIG-I, second repeat
    cd15805
    Location:805918
    RIG-I_C; C-terminal domain of Retinoic acid-inducible gene (RIG)-I protein, a cytoplasmic viral RNA receptor
    cl14633
    Location:292
    DD; Death Domain Superfamily of protein-protein interaction domains
    cl17041
    Location:243771
    helicase_insert_domain; helicase_insert_domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p12 Primary Assembly

    Range
    32455302..32526324 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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